| Summary: | <p>Abstract</p> <p>Background</p> <p><it>Thellungiella halophila </it>(also known as <it>T. salsuginea</it>) is a model halophyte with a small size, short life cycle, and small genome. <it>Thellungiella </it>genes exhibit a high degree of sequence identity with Arabidopsis genes (90% at the cDNA level). We previously generated a full-length enriched cDNA library of <it>T. halophila </it>from various tissues and from whole plants treated with salinity, chilling, freezing stress, or ABA. We determined the DNA sequences of 20 000 cDNAs at both the 5'- and 3' ends, and identified 9569 distinct genes.</p> <p>Results</p> <p>Here, we completely sequenced 1047 <it>Thellungiella </it>full-length cDNAs representing abiotic-stress-related genes, transcription factor genes, and protein phosphatase 2C genes. The predicted coding sequences, 5'-UTRs, and 3'-UTRs were compared with those of orthologous genes from Arabidopsis for length, sequence similarity, and structure. The 5'-UTR sequences of <it>Thellungiella </it>and Arabidopsis orthologs shared a significant level of similarity, although the motifs were rearranged. While examining the stress-related <it>Thellungiella </it>coding sequences, we found a short splicing variant of <it>T. halophila </it><it>salt overly sensitive 1 </it>(<it>ThSOS1</it>), designated <it>ThSOS1S</it>. ThSOS1S contains the transmembrane domain of ThSOS1 but lacks the C-terminal hydrophilic region. The expression level of <it>ThSOS1S </it>under normal growth conditions was higher than that of <it>ThSOS1</it>. We also compared the expression levels of Na<sup>+</sup>-transport-system genes between <it>Thellungiella </it>and Arabidopsis by using full-length cDNAs from each species as probes. Several genes that play essential roles in Na<sup>+ </sup>excretion, compartmentation, and diffusion (<it>SOS1</it>, <it>SOS2</it>, <it>NHX1</it>, and <it>HKT1</it>) were expressed at higher levels in <it>Thellungiella </it>than in Arabidopsis.</p> <p>Conclusions</p> <p>The full-length cDNA sequences obtained in this study will be essential for the ongoing annotation of the <it>Thellungiella </it>genome, especially for further improvement of gene prediction. Moreover, they will enable us to find splicing variants such as <it>ThSOS1S </it>(AB562331).</p>
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